Sequence bundled with its Kmer-based lookup index (same thing as old lookup table)

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@66 348d0f76-0448-11de-a6fe-93d51630548a

playground/java/src/org/broadinstitute/sting/indels/IndexedSequence.java

@@ -0,0 +1,95 @@
+package org.broadinstitute.sting.indels;
+
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.Map.Entry;
+
+public class IndexedSequence implements Iterable<Map.Entry<Short,List<Integer>>> {
+	private Map<Short,List<Integer> > m_locs;
+	private String m_seq;
+	private int m_K;
+	
+	public IndexedSequence(String seq, int K) {
+		m_locs = new Hashtable<Short,List<Integer> >();
+		m_seq = new String(seq);
+		m_K = K;
+		Iterator<Short> iter = new KmerCodeIterator(seq, K);
+		int offset = 0;
+		while ( iter.hasNext() ) {
+			Short k = iter.next();
+			List<Integer> offset_list = m_locs.get(k);
+			if ( offset_list == null ) { 
+				offset_list = new ArrayList<Integer>();
+				m_locs.put(k,offset_list);
+			}
+			offset_list.add(offset++);
+		}
+	}
+	
+	public Iterator<Entry<Short, List<Integer>>> iterator() {
+		return m_locs.entrySet().iterator();
+	}
+
+	public int length() { return m_seq.length(); }
+	
+	public List<Integer> getOffsets(short k) { return m_locs.get(k); }
+	
+	String getSequence() { return m_seq; }
+	
+	public int getK() { return m_K; }
+	
+	public static void testMe() {
+		String s = "ACCGTGCGGGCACCTGC";
+		int K = 3;
+		IndexedSequence is = new IndexedSequence(s,K);
+		System.out.println("Sequence: "+ s);
+		System.out.print("          ");
+		for ( int i= 0 ; i < s.length() ; i++ ) {
+			if ( i % 10 == 0 ) System.out.print(i/10);
+			else System.out.print(' ');
+		}
+		System.out.println();
+		System.out.print("          ");
+		for ( int i= 0 ; i < s.length() ; i++ ) System.out.print(i%10);
+		System.out.println();
+		System.out.println();
+	
+		System.out.println("Indexing with K="+K+":");
+		
+		Set< Map.Entry<Short, List<Integer> > > data  = is.m_locs.entrySet(); 
+		for ( Map.Entry<Short, List<Integer> > e : data ) {
+//			System.out.print("("+e.getKey()+") ");
+			System.out.print(kmerToString(e.getKey().shortValue(),K));
+			System.out.print("-->");
+			for ( Integer offset : e.getValue() ) {
+				System.out.print(" "+offset.toString());
+			}
+			System.out.println();
+		}
+	}
+	
+	private static String kmerToString(short code, int K) {
+		StringBuffer b = new StringBuffer(K);
+		for ( int i = 0 ; i < K ; i++ ) {
+			char c='N';
+			switch( code & 0x3 ) {
+			case 0 : c = 'A' ; break; 
+			case 1 : c = 'C' ; break; 
+			case 2 : c = 'G' ; break; 
+			case 3 : c = 'T' ; break; 
+			}
+			b.append(c);
+			code >>= 2;
+		}
+		return b.reverse().toString(); 
+	}
+	
+	public static void main(String argv[]) {
+		testMe();
+	}
+
+}